Search results for the GEO ID: GSE39733  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM978354 | GPL570 |
|
A549 siRNA FAM60A CNTRL 1
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: non-targeting
|
Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 1
|
| Sample_geo_accession | GSM978354
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978354/suppl/GSM978354_siCNTRL1_kts4_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
GSM978355 | GPL570 |
|
A549 siRNA FAM60A CNTRL 2
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: non-targeting
|
Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 2
|
| Sample_geo_accession | GSM978355
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978355/suppl/GSM978355_siCNTRL2_kts4_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
GSM978356 | GPL570 |
|
A549 siRNA FAM60A CNTRL 3
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: non-targeting
|
Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 3
|
| Sample_geo_accession | GSM978356
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978356/suppl/GSM978356_siCNTRL3_kts4_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
GSM978357 | GPL570 |
|
A549 siRNA FAM60A 1
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: FAM60A targeting
|
Gene expression from A549 cells after transfection with FAM60A targeting siRNA, replicate 1
|
| Sample_geo_accession | GSM978357
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978357/suppl/GSM978357_siFAM60A_1_kts4_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
GSM978358 | GPL570 |
|
A549 siRNA FAM60A 2
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: FAM60A targeting
|
Gene expression from A549 cells after transfection with FAM60A targeting siRNA, replicate 2
|
| Sample_geo_accession | GSM978358
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978358/suppl/GSM978358_siFAM60A_2_kts4_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
GSM978359 | GPL570 |
|
A549 siRNA FAM60A 3
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: FAM60A targeting
|
Gene expression from A549 cells after transfection with FAM60A targeting siRNA, replicate 3
|
| Sample_geo_accession | GSM978359
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978359/suppl/GSM978359_siFAM60A_3_kts4_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
GSM978360 | GPL570 |
|
A549 siRNA SDS3 CNTRL 1
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: non-targeting
|
Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 1
|
| Sample_geo_accession | GSM978360
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978360/suppl/GSM978360_1_siCNTRL1_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
GSM978361 | GPL570 |
|
A549 siRNA SDS3 CNTRL 2
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: non-targeting
|
Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 2
|
| Sample_geo_accession | GSM978361
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978361/suppl/GSM978361_2_siCNTRL2_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
GSM978362 | GPL570 |
|
A549 siRNA SDS3 CNTRL 3
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: non-targeting
|
Gene expression from A549 cells after transfection with non-targeting siRNA, replicate 3
|
| Sample_geo_accession | GSM978362
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978362/suppl/GSM978362_3_siCNTRL3_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
GSM978363 | GPL570 |
|
A549 siRNA SDS3 1
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: SDS3 targeting
|
Gene expression from A549 cells after transfection with SDS3 targeting siRNA, replicate 1
|
| Sample_geo_accession | GSM978363
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978363/suppl/GSM978363_4_siSDS3_1_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
GSM978364 | GPL570 |
|
A549 siRNA SDS3 2
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: SDS3 targeting
|
Gene expression from A549 cells after transfection with SDS3 targeting siRNA, replicate 2
|
| Sample_geo_accession | GSM978364
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978364/suppl/GSM978364_5_siSDS3_2_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
GSM978365 | GPL570 |
|
A549 siRNA SDS3 3
|
A549 lung cancer cells
|
cell line: A549
cell type: human lung cancer
sirna: SDS3 targeting
|
Gene expression from A549 cells after transfection with SDS3 targeting siRNA, replicate 3
|
| Sample_geo_accession | GSM978365
| | Sample_status | Public on Sep 15 2012
| | Sample_submission_date | Jul 30 2012
| | Sample_last_update_date | Sep 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | A549 cells were transfected one day after plating using 50 nM siRNAs (Ambion non-targeting siRNA (AM4637); FAM60A siRNA (s33909)) and Dharmafect 1 transfection reagent.
| | Sample_growth_protocol_ch1 | 7.5x10^4 A549 cells were plated in each well of a 6-well plate. Cells were plated in F-12K media (Cellgro) with 10% FBS in triplicate.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.
| | Sample_data_processing | Array intensities were processed using the RMA algorithm in R/bioconductor.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chris,W,Seidel
| | Sample_contact_email | seidel@phageT4.org
| | Sample_contact_phone | 816 926 9054
| | Sample_contact_laboratory | Seidel
| | Sample_contact_department | Genomics
| | Sample_contact_institute | Stowers Institute
| | Sample_contact_address | 1000 E 50th St
| | Sample_contact_city | Kansas City
| | Sample_contact_state | MO
| | Sample_contact_zip/postal_code | 64110
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM978nnn/GSM978365/suppl/GSM978365_6_siSDS3_3_HG-U133_Plus_2.CEL.gz
| | Sample_series_id | GSE39733
| | Sample_data_row_count | 54675
| | |
|
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